SMTL ID : 1muq.2 (1 other biounit)

X-ray Crystal Structure of Rattlesnake Venom Complexed With Thiodigalactoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

1 x GAL- YIO: 1-thio-beta-D-galactopyranose-(1-1)-beta-D-galactopyranose(Non-covalent)

GAL-YIO.1: 7 residues within 4Å: Chain B: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.96, B:E.104, B:N.119

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.98, A:E.104, A:D.120, A:D.120 CA.5: 6 residues within 4Å: Chain B: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL-YIO.1 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.98, B:E.104, B:D.120, B:D.120 CA.7: 6 residues within 4Å: Chain C: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.98, C:E.104, C:D.120, C:D.120 CA.10: 5 residues within 4Å: Chain D: Q.96, D.98, E.104, N.119, D.120 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.104, D:D.120 CA.12: 6 residues within 4Å: Chain E: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.14 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.98, E:E.104, E:D.120, E:D.120

5 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: Y.15, S.42, H.44, Q.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.42, A:S.42 NA.6: 4 residues within 4Å: Chain B: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.42, B:S.42 Water bridges: B:S.42 NA.8: 4 residues within 4Å: Chain C: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.15, C:S.42, C:S.42 NA.11: 4 residues within 4Å: Chain D: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.15, D:S.42, D:S.42 NA.13: 4 residues within 4Å: Chain E: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.15, E:S.42, E:Q.132

3 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.4: 8 residues within 4Å: Chain A: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.96, A:E.104, A:N.119, A:Q.121 Water bridges: A:N.119 GAL.9: 8 residues within 4Å: Chain C: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.96, C:E.104 Water bridges: C:Q.121, C:Q.121 GAL.14: 7 residues within 4Å: Chain E: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.96, E:E.104, E:N.119, E:N.119, E:Q.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walker, J.R. et al., X-ray Crystal Structure of a Galactose-Specific C-Type Lectin Possessing a Novel Decameric Quaternary Structure. Biochemistry (2004)

Release Date

2003-07-01

Peptides

Galactose-specific lectin: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Galactose-specific lectin

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